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    <title>Visualization - TIC/XIC visualizer</title>
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<h1>TIC/XIC visualizer</h1>

<h2>Description</h2>

<p>
    This tool displays a two-dimensional plot, where the <em>x</em>-axis corresponds to retention time and the
    <em>y</em>-axis is the intensity level of the signal. This visualization of the raw data corresponds to the
    chromatographic appearance of the data.
</p>

<p>
    This type of plot is generally used in MZmine to display chromatographic peaks.
</p>

<h4>Parameters</h4>

<dl>
    <dt>Raw data files</dt>
    <dd>List of raw data files to display in the TIC visualizer, with the possibility of choosing one, many or all of
        them. The TIC will display all the chromatograms in the same plot.
    </dd>

    <dt>MS level</dt>
    <dd>This refers to the scan level (MS<sup>1</sup>,MS<sup>2</sup>,... ,MS<sup>n</sup>) to display in the plot.</dd>

    <dt>Plot type</dt>
    <dd>Type of <em>y</em>-axis value calculation. <em>TIC</em> shows the sum of intensities, <em>base peak</em> shows
        the maximum intensities.
    </dd>

    <dt>Retention time</dt>
    <dd>Retention time (<em>x</em>-axis) range.</dd>

    <dt>m/z range</dt>
    <dd>Range of m/z values. If this range does not include the entire scan m/z range, the resulting visualizer is XIC
        type.
    </dd>

    <dt>Selected peaks</dt>
    <dd>List of chromatographic peaks to display in the TIC visualizer. This list is available only if a peak list
        related to the selected raw data file exists in the current project.
    </dd>
</dl>

<p>
    Additionally, the parameters window has a <em>Set automatically</em> button that allows you to set all the ranges
    to the maximum ranges represented in the raw data.

<p>

<h4>Functionality</h4>

<p>
The following zoom functions are available:
</p>

<ul>
<li>Use the + or - key on the keyboard to zoom in or out.</li>
<li>Scroll with the mouse to zoom in or out.</li>
<li>Drag the mouse from left to right to select the area to zoom in.</li>
<li>Drag the mouse from right to left to zoom out to the default view.</li>
<li>Single click on the y-axis to auto set the intensity to auto height.</li>
<li>Double click on the y- or x-axis to reset the zoom to default.</li>
</ul>

<p>
    <img src="TIC_zoom.png" alt="Zoom function">
</p>

<p>
    To the right of the plot is a set of buttons whose functionality is also available via a pop-up menu that appears
    when you click the right-mouse button in the plot area.
</p>

<p>
    When the mouse cursor passes over a plot line or peak, a tool-tip is displayed with information about the data
    point. Left-clicking will select a data point in the plot. Using the top button from the right panel it is possible
    to visualize the mass spectrum for the selected data point. Double-clicking near a data point will have the same
    result.
</p>

<p>
    <img src="TIC_scan.png" alt="Mass spectrum function">
</p>

<p>
    Use the second button on the right panel to display a marker for each data point.
</p>

<p>
    <img src="TIC_toggle.png" alt="Display data point markers">
</p>

<p>
    Use the third button on the right panel to display labels on the data points. By default m/z labels are displayed
    for major peaks. If the plot includes selected peaks from a peak list then those peaks can be labeled with their
    identities. Pressing the labels button will cycle between displaying m/z labels, peak identity labels (if any) or no
    labels.
</p>

<p>
    Use the fourth button in the right panel to manually modify the axis ranges.
</p>

<p>
    It is possible to display data from other raw data files by using the <em>Add plot of file...</em> item from the
    pop-up menu.
</p>

<p>
    <img src="TIC_submenu.png" alt="Add plot of file menu">
</p>

<p>
    <img src="TIC_double_plot.png" alt="Multiple data files plot">
</p>

<p>
    The pop-up menu also includes a <em>Set same range to all windows</em> item, which applies the same ranges to all
    TIC plot windows in the current project.
</p>

<p>The submenu also includes an <em>Export chromatogram...</em> item that allows you to select a chromatogram to export.
    Choose a chromatogram and you'll be prompted to select a file name to export the chromatogram values (RT, intensity) to.
</p>

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